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Friday, December 29, 2017

If you buy a Haplotee or any other DNAGeeks merchandise through this blog via this LINK, I'll get some cash.
Why is this important? Because 2018 is going to be a huge year for population genetics, and especially for ancient DNA, and if this blog is also going to be huge, then I'll need some money. So if you like this blog, or even if you hate it, but you like spending time here hating it, then buy a Haplotee. Or several.

Please note also that I've recently launched a genetic ancestry online store, which will be updated regularly with different tests throughout the year (see here). By purchasing tests from the store, you'll not only be helping to make this blog awesome, but also getting amongst the most accurate ancestry analyses available anywhere. Thank you for your support.

Monday, December 18, 2017

David W. Anthony has just posted a new paper at his Academia.edu page titled Archaeology and Language: Why Archaeologists Care about the Indo-European Problem (see here).
It's not only an interesting discussion about why the search for the Indo-European homeland is still such a big deal, but also a useful, almost up to date, summary of the fascinating stuff that ancient DNA has revealed about the genetic history of Europe, with a special focus on the origin of the Corded Ware people, who are generally accepted to be the first Indo-European-speaking population of Northern Europe.
Now, I say it's an almost up to date summary, because Anthony seems fairly certain that the Corded Ware people were descendants of the Yamnaya people, rather than just their close relatives. He uses archaeological and ancient DNA data to argue that Yamnaya migrants moved from the North Pontic steppe to the eastern Carpathian Basin (present-day Hungary), and then onto what is now southern Poland to give rise to the proto-Corded Ware population.
I probably would've said this was a highly plausible scenario before I saw the ancient DNA results from the latest preprint of Mathieson et al. 2017, an ancient genomics paper in the works focusing on Southeastern Europe (see here). But now that I've seen those results, I feel that Anthony's proposal might be outdated.
One of the samples in that preprint is from a pre-Yamnaya Eneolithic burial on the northern edge of North Pontic steppe, in what is now eastern Ukraine, labeled Ukraine_Eneolithic I6561. This individual not only strongly resembles the Corded Ware people in terms of genome-wide genetic structure, but also belongs to Y-haplogroup R1a-M417, which is a paternal marker probably no older than the Eneolithic and intimately associated with the Corded Ware expansion. Currently, as far as I can see, he's by far the most likely candidate in the ancient DNA record to belong to a proto-Corded Ware population.
Keep in mind also that not a single instance of R1a-M417 has yet been found among a wide range of prehistoric individuals from the Carpathian Basin. On the other hand, Olalde et al. 2017 (see here) did manage to catch one Early Bronze Age (EBA) Bell Beaker from the region belonging to R1b-Z2103, which is the paternal marker currently most strongly associated with Yamnaya.
Below is a map of Central and Eastern Europe ca. 3000-2000 BCE from Anthony's paper, edited by me to show the burial location of Ukraine_Eneolithic I6561. If we assume that his descendants or close relatives were the proto-Corded Ware population, then looking at this map, it seems unlikely to me that they would've taken the Carpathian Basin route before expanding into Northern Europe. Rather, I'd say that they would've fanned out across the north directly from the steppe, perhaps along those northward-pointing river valleys? And I suspect that they may have still been a pre-Yamnaya group as they migrated out of the steppe, just as Yamnaya was forming somewhere to the east.

Friday, December 15, 2017

Here's a map from yesterday's presentation by Italian archaeologist Massimo Vidale at the MPI-SHH Jena Cross Roads conference on South Asia. He was focusing on the skeletal remains from the protohistoric, and likely early Indo-Aryan, cemeteries at Udegram and Gogdara in the Swat Valley, modern-day Pakistan. Source: Twitter.

And this is my own map from back in August (see here) summarizing what ancient DNA (both published and otherwise...nudge, nudge) is telling us about the early Indo-European, including Indo-Aryan, expansions across Eurasia.

Friday, December 1, 2017

Several South Central Asian populations have a reputation for producing individuals who look surprisingly European, even the lighter shade sort of European from Eastern and Northern Europe. This is especially true of the Pamiri Tajiks, and that's unlikely to be a coincidence, because these people probably do harbor a lot of ancient Eastern European ancestry.
My own estimates, using various ancestry modeling methods, suggest that Pamiri Tajiks derive ~50% of their genome-wide genetic ancestry from populations closely related to, and probably derived from, Eneolithic/Early Bronze Age pastoralists from the Pontic-Caspian steppe of Eastern Europe, such as the Sredny Stog and Yamnaya peoples. Below is a simple Admixture graph using the mostly Yamnaya-derived Iron Age Sarmatians from Pokrovka, Russia, in far Eastern Europe, to illustrate the point. Note that Sarmatians were East Iranic-speakers, which is what Pamiri Tajiks are. The relevant graph file is available here.

But, some of you might retort, this is all just statistical smoke and mirrors, and what it really shows is that these so called Europeans came from Central Asia or even India.
Not so, because my models can't be twisted any which way, and they have strong support from uniparental marker data.
Many South Central Asian groups, and especially Indo-European-speakers, like the Tajiks, show moderate to high frequencies of two Y-chromosome haplogroups typical of Bronze Age Eastern Europeans: R1a-M417 and R1b-M269. This is old news to the regular visitors here and its implications are obvious, so if you still think that these haplogroups expanded from South Central Asia to Eastern Europe, rather than the other way around, then please update yourself (for some pointers, see here and here).
And now, courtesy of Peng et al. 2017, we also have a much better understanding of ancient European influence on the maternal gene pool of Pamiri groups (see here). The paper doesn't specifically cover the topic of European admixture in South Central Asia, but it nevertheless demonstrates it unequivocally.
Below are a couple of phylogenetic trees from the paper featuring a wide range of mitochondrial DNA (mtDNA) sequences shared between Europeans and Central and South Asians; quite a few of these lineages are rooted in Eastern Europe, as shown by both modern-day and ancient DNA, so they strongly imply gene flow, and indeed considerable maternal gene flow, from Eastern Europe deep into Asia.

Tuesday, November 28, 2017

Two former Harvard scientists Pontus Skoglund and Iain Mathieson are working on a new review paper on the wide range of scientific breakthroughs provided by ancient genomics over the past decade. The preprint is available at Dropbox here. There's also a thread about the preprint at Mathieson's Twitter account here.
I've read through it a couple of times, especially the parts about Europe, and haven't been able to spot any major problems; the authors obviously chose their words very carefully, and their geography is beyond reproach. [Edit: first problem spotted, see here]
Now, you might think that geography is easy, but apparently not when it comes to the location of the Pontic-Caspian steppe. Recent media articles have claimed that it's located in West Asia, and, I kid you not, even that it's hilly (for instance, see here), while scientists from Max Planck and other supposedly high brow places seem to think that it's in Central Eurasia (see here). Nope, as Skoglund and Mathieson correctly point out, it's actually located in (far) Eastern Europe, while Central Eurasia is generally posited to be further to the east. From the preprint (emphasis is mine):

Anatomically modern humans were widely distributed in Europe by at least 42,000-45,000 BP (3; 41). The oldest genomic data from a modern human in Europe is the Oase 1 individual from present-day Romania dated to 37,600-41,600 BP. This individual, which had a direct Neanderthal ancestor in the past four to six generations, did not contribute detectable ancestry to later Upper Paleolithic populations (24). During the Upper Palaeolithic, a major transformation ~30,000-35,000 years ago was likely associated with the replacement of the Aurignacian with the Gravettian culture in western Europe(28). As the Last Glacial Maximum (LGM) came to an end and the ice sheets receded, Europe was repopulated, possibly from southern European and central Eurasian refugia (28). Another transformation may have taken place during an interstadial warm period ~14.5 kya, replacing the original recolonizers with a population that would come to form the Mesolithic populations of Europe (28; 93). These Mesolithic populations were outside the genetic diversity of present-day Europe (114; 131) and themselves display a clinal structure, with an east-to-west cline (32; 37; 38; 47; 57; 62; 72; 78; 112; 130). The origin of this cline is not clear, although it plausibly reflects two or more major sources of ancestry in the post-LGM or post-14.5kya expansions.
Starting from the southwest around 8,500 BP, the Mesolithic ancestry of Europe was largely replaced (29; 38; 42; 130; 131) as a new type of ancestry related to that found in Neolithic northwest Anatolia (73; 87) and, ultimately, to early farming populations of the Levant and Northern Iran (11; 56) expanded throughout Europe. This ancestry rapidly reached the extreme edges of Europe, with direct evidence of its presence in Iberia at 7300 BP (86), in Ireland at 5100 BP (14) and in Scandinavia at 4900 BP (131). This “Anatolian Neolithic” ancestry was highly diverged relative to the “hunter-gatherer” ancestry of the populations that previously inhabited Europe (F ST ~ 0.1, similar to the divergence between present-day European and East Asian populations) (73; 132). Across Europe, its appearance was closely linked in time and space to the adoption of an agricultural lifestyle, and it now seems established that this change in lifestyle was driven, at least in part, by the migration. However, the Anatolian Neolithic migrants did not replace the hunter-gatherer populations. Over the next 4000 years, the two populations merged, and by 4500 BP, almost all European populations were admixed between these two ancestries, typically with 10-25% hunter-gatherer ancestry (29; 38; 42; 50; 62; 71; 73; 130; 131). Across Europe, this “resurgence” of hunter-gatherer ancestry (10) was independent–driven by local hunter-gatherer populations who lived in close proximity to farming groups (7; 62; 72; 130).
The next substantial change is closely related to ancestry that by around 5000 BP extended over a region of more than 2000 miles of the Eurasian steppe, including in individuals associated with the Yamnaya Cultural Complex in far-eastern Europe (1; 38) and with the Afanasievo culture in the central Asian Altai mountains (1). This “steppe” ancestry is itself a mixture between ancestry that is related to Mesolithic hunter-gatherers of eastern Europe and ancestry that is related to both present-day populations (38) and Mesolithic hunter-gatherers (46) from the Caucasus mountains, and also to the populations of Neolithic (11), and Copper Age (56) Iran. Steppe ancestry appeared in southeastern Europe by 6000 BP (72), northeastern Europe around 5000 BP (47) and central Europe at the time of the Corded Ware Complex around 4600 BP (1; 38). These dates are reasonably tight constraints, because in each case there is no evidence of steppe ancestry in individuals immediately preceding these dates (47; 72). Gene flow on the steppe was extensive and bidirectional, as shown by the eastward flow of Anatolian Neolithic ancestry–reaching well into central Eurasia by the time of the Andronovo culture ~3500 BP (1)–and the westward flow of East Asian ancestry–found in individuals associated with the Iron Age Scythian culture close to the Black Sea ~2500 BP (143).
Copper and Bronze Age population movements (14; 78 Martiniano, 2017 #8761; 85; 112), as well as later movements in the Iron Age and Historical period (70; 119) further distributed steppe ancestry around Europe. Present-day western European populations can be modeled as mixtures of these three ancestry components (Mesolithic hunter-gatherer, Anatolian Neolithic and Steppe) (38; 57). In eastern Europe, further shifts in ancestry are the result of additional or distinct gene flow from Anatolia throughout the Neolithic and Bronze Age in the Aegean (42; 51; 55; 72; 87), and gene flow from Siberian-related populations in Finland and the Baltic region (38).

And I really like this part; sounds ominous for the Out-of-India (OIT) crowd, doesn't it? Hopefully we won't have to wait too long for the relevant paper from Harvard, which, I can assure you, is coming sooner or later.

There are no published ancient DNA studies from South- or Southeast Asia. However, data from neighboring regions provides clues to the population history of this region. In particular, present-day South Asian populations share ancestry with Neolithic Iranian (11) and Steppe (56) populations. This strongly suggests Neolithic or Bronze Age contact between South Asia and west/central Eurasia, although only direct ancient DNA evidence from the region will resolve the timing and structure of this contact.

Wednesday, November 22, 2017

Max Planck's Thiseas Christos Lamnidis recently tweeted this image of a part of a poster that he's presenting on the population history of Northeastern (NE) Europe at the Human Evolution 2017 conference in Cambridge, UK (for the tweet see here):

If you can't make out the text in the image, this is what the introduction says:

European history has been shaped by migrations, and subsequent admixture. Evidence points to migrations linked to the advent of agriculture, and the spread of Indo-European languages [a b]. Little is known about the ancient population history of NE Europeans, specifically Uralic speakers. Here we analyse eleven ancient genomes from Finland and NW Russia and a high-coverage modern Saami genome, and show that northern Europe was shaped by gene flow from Siberia that began at least 3,500 ya. Today, this ancestry is found in modern populations of the region, especially Uralic speakers. Additionally, we show that ancestors of the Saami inhabited a larger territory in Finland during the Iron Age than today.

It's intriguing to me that Max Planck is looking so closely at these issues now, because back in 2015 I ripped into Max Planck's Paul Heggarty for some comments that he made about the potential link between Yamnaya-related admixture and Uralic languages (see here). This is what I said back then:

These are exceedingly naive and stupid comments from someone representing the Max Planck Institute. Perhaps as an ardent supporter of the Anatolian hypothesis he's feeling more than a little desperate at this point and clutching at straws? That's because anyone with even a basic grasp of European linguistics and genetics should know that:
- present-day Hungarians and Estonians speak Uralic languages, but they are of course overwhelmingly of Indo-European origin, which is easily seen in their genome-wide and uniparental DNA
- other Uralic speakers, further to the north and east, in the forest zone away from Indo-European influence, are clearly distinct from the vast majority of Indo-European speaking Europeans, because they show significant levels of recent Siberian ancestry, which was missing among the Yamnaya and Corded Ware people, and appears to be an Uralic-specific genetic signature
- therefore, it's highly unlikely that Uralic-speakers were also part of the Yamnaya > Corded Ware movement; rather, early Uralics in all likelihood began to move west across the forest zone well after the Yamnaya and related expansions from the steppe.

Monday, November 13, 2017

Considering the increasingly large numbers of paleogenomic samples being released online nowadays, it's no longer practical for me to try to highlight most archaeological cultures and even genetic clusters in my Principal Component Analyses (PCA) of the ancient world. Thus, from now on, I'll be focusing attention in such PCA on the main population shifts that have led to the formation of the modern-day West Eurasian gene pool and genetic substructures, like on the PCA plot below, which includes the new Lipson et al. 2017 data (available at the Reich Lab here).

The relevant PCA datasheet can be gotten here. By grouping several hundred ancient samples into just nine clusters, I'm attempting to highlight four key processes and resulting genetic shifts in Europe, the Near East and Central Asia:

- European forger populations mixing with genetically much more southern early farmers of Near Eastern origin, mostly during the Neolithic, bringing about the total disintegration of the Europe to Siberia Hunter-Gatherer cline
- "Old Europeans" being overrun and largely absorbed by Y-haplogroup R1-rich Kurgan pastoralists from the Pontic-Caspian steppe during the Eneolithic and Bronze Age, leading to the formation of at least one major new cline from the Bronze Age steppe into post-Kurgan expansion Europe
- the ancient Near East "imploding" or becoming significantly more compact in terms of genetic structure, likely due to a variety of major population expansions from the chalcolithic onwards from the eastern and western parts of the Fertile Crescent, as well as probably the Caucasus and Europe (note how the post-Neolithic western Asian cluster stretches out towards Europe)
- fully nomadic and very wide ranging pastoral and warrior cultures dominating the entire Eurasian steppe during the Iron Age, leading to the emergence of progressively more East Asian-admixed populations from west to east across the Eurasian steppe

An interesting outcome of the denser sampling from space and time in West Eurasia is that Y-haplogroup R1b, once so elusive in the ancient DNA record, is now popping up all over the place. The new Lipson et al. dataset, for instance, includes two R1b "Old Europeans" from Blatterhole in Germany dated to the Middle Neolithic. Below is the same PCA as above except with all of the ancients belonging to R1b marked with an X. The two Blatterhole samples are sitting in the largely empty space between the European/Siberian Hunter-Gatherer cline and most of the "Old Europe" cluster. The relevant PCA datasheet is available here.

So it may seem that we're back to square one in the long running effort to pinpoint the origin of Y-haplogroup R1b-L51, which encompasses almost 100% of modern-day Western European R1b lineages, and thus probably ranks as Europe's most common Y-haplogroup. But at this stage I'd say no, because R1b-L51 is a subclade of R1b-M269, of which the oldest sample comes from the Bronze Age steppe. In fact, as can be seen in the above PCA, this sample is sitting in exactly the right spot to be one of those pastoralists who overran "Old Europe", or at least a very close relative thereof.
Or am I wrong? Feel free to let me know in the comments.
I didn't bother creating a similar plot of ancient samples belonging to Y-haplogroup R1a, because, unlike R1b, this marker is still non-existent in samples from outside of Eastern Europe and Siberia dating to before the late Neolithic. And I doubt that this is simply due to a lack of the right ancient material. Moreover, the recent discovery of Y-haplogroup R1a-M417, which encompasses almost 100% of all modern-day R1a lineages on the planet, in a North Pontic steppe sample belonging to the Eneolithic Sredny Stog culture means that it's game over for the naysayers as far as the steppe origin of most modern-day R1a lineages is concerned (see here and here).
In other words, if you're still hoping to see R1a, and especially R1a-M417, pop up in non-steppe derived ancient individuals in, say, such far away places as South Asia, then you'll probably be waiting forever.
For the linguistic implications of all of this, see...
Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...Update 15/11/2017: After a couple of days of messing around with the Lipson et al. dataset, I'm certain that Late Copper Age sample Protoboleraz_LCA I2788 shows significant steppe-related admixture. This is the only sample from Lipson et al. with such an obvious signal of steppe-related input that had enough data to be analyzed individually by me with PCA and D-stats.

For the time being, amongst the best proxies for this signal appear to be Yamnaya_Samara and Samara_Eneolithic. But it's likely that the real source of the admixture is yet to enter the ancient DNA record, or at least my dataset. When it does, it'll probably be an Eneolithic pastoralist population from the North Pontic steppe.

Yamnaya_Samara also gives the best statistical fit as the single source population in qpAdm (see here). It's an important result, because it suggests that steppe peoples very similar to Yamnaya were already expanding on and out of the steppe as far back as ~3500 BCE, and perhaps a few hundred years earlier.
See also...
Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)

Thursday, November 9, 2017

Below is an abstract from the upcoming Human Evolution 2017 conference (Cambridge, UK, November 20-22). It'll be interesting to see when the paper comes out how Harney, Patterson et al. uncovered the Greek affinities of some of these individuals; uniparental markers, rare alleles? The accompanying pic is from Wikipedia.

The skeletons of Roopkund Lake: Genomic insights into the mysterious identity of ancient Himalayan travelers
Eadaoin Harney, Niraj Rai, Nick Patterson, Kumarasamy Thangaraj, David Reich
The high-altitude lake of Roopkund, situated over 5000 meters above sea level in the Himalayas, remains frozen for almost 11 months out of the year. When it melts, it reveals the skeletons of several hundred ancient individuals, thought to have died during a massive hail storm during the 8th century, A.D. There has been a great deal of speculation about the possible identity of these individuals, but their origins remain enigmatic. We present genome-wide ancient DNA from 17 individuals from the site of Roopkund. We report that these individuals cluster genetically into two distinct groups-consistent with observed morphological variation. Using population genetic analyses, we determine that one group appears to be composed of individuals with broadly South Asian ancestry, characterized by diffuse clustering along the Indian Cline. The second group appears to be of West Eurasian related ancestry, showing affinities with both Greek and Levantine populations.

Tuesday, October 31, 2017

It's an unfortunate reality that most commercial genetic ancestry tests out there are rather lame. They're not wrong per se, but that's probably the best that can be said about them. And let's be honest, that's no longer enough considering how far this area of science has come in recent years.
To try and remedy this problem, I'll be offering a wide range of highly accurate and unique, but low cost, ancestry tests here, in my makeshift online store, based on analyses on this blog. These tests will focus on either recent or ancient ancestry, or both, using the latest reference samples from scientific literature whenever possible. To make a purchase, send your request, autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and money (via PayPal) to eurogenesblog at gmail dot com.
Let's start things rolling with my genetic and linguistic landscape of Europe north of the Alps, Balkans and Pyrenees (see here). For a mere $6 USD I will pinpoint your location on the plot below amongst a variety of modern-day and ancient individuals. You'll also receive the principal component coordinates, which you can use to model your ancestry proportions (for instance, like here). Please keep in mind, however, that to ensure sensible results in this particular analysis, practically all of your ancestry has to derive from Central, Eastern and/or Northern Europe. Most of my other tests won't be so restrictive.

I'll be updating this plot regularly with many more ancient samples as they become available, but your coordinates will remain relevant as I do so.
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Following a rigorous testing phase, the awesome Global 25 analysis is now available at the store for $12 USD (see here). What's so awesome about this test, you might ask? See here and here.

Please send your request, autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and money (via PayPal) to eurogenesblog at gmail dot com.
However, note that this test is free for anyone who already has Global 10 coordinates (see here). That's right, if you already have Global 10 coordinates, all you have to do is to send me your data and say what it's for. Simple as that.
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The popular Basal-rich K7 admixture test is now available via the store for $6 USD. It's suitable for everyone, except people with significant (>10%) Sub-Saharan ancestry. For more information about this test and some ideas about what to do with the output see here and here.

Monday, October 30, 2017

In this study, we examine trauma on human remains from the Tripolye site of Verteba Cave in western Ukraine. The remains of 36 individuals, including 25 crania, were buried in the gypsum cave as secondary interments. The frequency of cranial trauma is 30-44% among the 25 crania, six males, four females and one adult of indeterminate sex displayed cranial trauma. Of the 18 total fractures, 10 were significantly large and penetrating suggesting lethal force. Over half of the trauma is located on the posterior aspect of the crania, suggesting the victims were attacked from behind. Sixteen of the fractures observed were perimortem and two were antemortem. The distribution and characteristics of the fractures suggest that some of the Tripolye individuals buried at Verteba Cave were victims of a lethal surprise attack.
...
Recent paleogenomic studies have indicated that the nomadic pastoralists of the Pontic-Caspian steppe were involved in large-scale population movements at precisely this time, expanding westward farther into continental Europe (Haak et al., 2015). Such a massive population movement likely resulted in lethally violent interactions between indigenous populations and the newly arriving migrants.

I feel that I need to do a double take, and demonstrate more obviously why my new PCA, the one that I introduced in the recent Tollense Valley warrior blog post (see here), should prove very useful for analyzing both genetic and ethnolinguistic links in Northern Europe between modern-day populations and ancient samples, particularly those from late prehistory to early history, which is when the main ethnolinguistic groups that today dominate Northern Europe formed. Judging by some of the reactions in the comments, not everyone was convinced, so let's try this again.
Below is a new version of the said PCA that focuses on several ancient individuals who, based on their archaeological contexts, should show strong genetic affinities to modern-day speakers of Celtic, Germanic and Slavic languages in Northern Europe. These are three Iron Age samples from what is now England, one Iron Age sample from what is now Sweden, and two Medieval samples from what is now Bohemia, Czech Republic, respectively. The relevant datasheet is available here.

And clearly these ancients do show the expected genetic affinities considering where they cluster relative to modern-day Northern Europeans in the two most significant dimensions of genetic variation. Moreover, despite the fact that the Anglo-Saxon and English Iron Age samples were all excavated from sites in eastern England, the Anglo-Saxons cluster between the English Iron Age individuals and the singleton Scandinavian Iron Age sample. This of course makes perfect sense, considering that the Anglo-Saxons were Germanic speakers with recent ancestry from very near to Scandinavia.
So everything seems in good order, and for now it's very difficult for me to consider that those Tollense Valley warriors who cluster alongside modern-day Slavic speakers on my PCA are not ethnolinguistically closer to them than to Celtic and Germanic speakers.
On the other hand, my standard PCA of West Eurasian genetic variation does a comparatively lousy job at matching ethnolinguistic origins with genetic structure, at least in Northern Europe. Note below, for instance, that the same Celtic and Germanic samples from England and Scandinavia form a tight cluster between the two Slavs from Bohemia. Hence, based on this PCA it would be very difficult, perhaps impossible, to correctly predict the ethnolinguistic ties of these ancients just by looking where they cluster relative to modern-day Germanics, Slavs and so on. Right click and open in a new tab to enlarge to the max.

Saturday, October 28, 2017

The series of maps below is from a new paper by Liebert et al. at Human Genetics. Almost certainly, any population with a sizable level of the 13910*T allele has relatively recent (post-Mesolithic) ancestry from Europe. In that context, note the presence of 13910*T in South Asia and North Central Africa. Populations in these regions also show high frequencies of two Y-chromosome haplogroups that are present in samples from Mesolithic Eastern Europe: R1a and R1b-V88, respectively. It's hard to imagine that this is a coincidence.

Thursday, October 26, 2017

Summary: The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1, 2, 3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6, 7, 8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th–11th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%–31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.

This is strongly suggested by the Principal Component Analysis (PCA) below, which shows that many of the Tollense Valley warriors (Welzin_BA) cluster in the Slavic-specific part of the plot. The relevant datasheet is available here.

I designed this PCA with the sole purpose of using Balto-Slavic-specific genetic drift to differentiate Slavs from Germans, except of course those Germans with a lot of Slavic ancestry, who are usually from eastern Germany and Austria. I can assure you, people who don't harbor significant Slavic ancestry never cluster in this part of the plot.
The only other ancient samples that cluster in the Slavic zone are, as expected, an early Slav from Bohemia and, interestingly, a Bronze Age individual from what is now Hungary. But we've already seen strong genetic, and indeed genealogical, links between another Hungarian Bronze Age genome and present-day Slavs (see figure 3 here).
So what's going on? Did the proto-Slavs come into existence during the Bronze Age, as opposed to the more generally accepted early Medieval Period? And did they expand from what is now Hungary? Or did they migrate there from the Baltic region? Thanks to Matt in the comments for the table below.

I blogged about the Tollense Valley project last year, following a Science feature which posited that the battle fallen may have come from very different parts of Europe (see here). But judging by the results in this thesis, that might not be the case after all. Emphasis is mine:

The 21 samples available to this study stem from skeletal remains found in the Tollense valley in north eastern Germany and date to the bronze age (ca. 3200 BP), except for sample WEZ16, which dates to the neolithic (ca. 5000 BP) and was found in a burial context. Although several samples from the Welzin site have been dated using the C 14 method, from the samples used for this study only the neolithic WEZ16 (2960BC ±66) and the Bronze Age sample WEZ15 (1007BC ±102) were radiocarbon dated. All individuals except WEZ16 were found in a non burial context, widely dispersed and dis-articulated [48] along the river bank of the Tollense river.
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The PCA in Figure 4.24 shows modern Eurasian individuals in grey and ancient individuals in colour according to their assigned population (for details on the modern populations see Figure A.48). The majority of Welzin individuals fall within the variation of modern populations from the northern central part of Europe (compare Figure A.48), with hunter gatherers, the Yamnaya and the LBK populations appearing on the outer range of PC1 and PC2.
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Outliers from the Welzin cluster are: WEZ16, which falls closer to the Sardinians and neolithic LBK along PC2, WEZ54, which clusters with the Basques and also fall closer to LBK individuals along PC2, WEZ57, which falls in between the former individual and the Welzin cluster, and WEZ56, which separates from the main cluster of Welzin individuals along PC2 in the opposite direction as the former three, towards the Corded Ware or Yamnaya.
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The ancient population that share the most drift with the Welzin group are WHG and the SHG population followed by the Unetice, the Bell Beaker and the Corded Wear. Starting with the Unetice the following f3 values fall in the range of the standard error of each other. The average difference between two consecutive f3 values is 0.0021 ± 0.0024 and the average standard error in each f3 value is 0.0037 ± 0.0007. The most similar modern populations are the Polish, Austrians and the Scottish.
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Any interpretation regarding possible parties that might have been involved in the conflict in the Tollense valley ∼ 3200 ago can only be speculative with regards to the here shown data. With the resolution given here, an educated guess for different involved parties could be, that both parties were relatively local and more closely related than any ancient DNA study was able to separate so far. Maybe similar to people from Hessen versus people from Rhineland-Palatinate in modern Germany.

Friday, October 20, 2017

The mad scientists are at it again. The quote below is from an American Society of Human Genetics (ASHG) talk abstract. For the whole thing see here. Now, as I've pointed out on this blog before, Finns do not have Buryat or Mongolian ancestry, or anything even closely related dating to the Middle Ages. What they do have is some sort of Siberian admixture, which has been poorly characterized to date, but is probably associated with archaeologically attested population movements across northern Eurasia during the metal ages.

We identified significant gene flow from the Buryats to the Finnish which was predicted to be occurred in 1,228 (±87) year. Moreover, 13.38% of Buryat admixture was predicted in the Finnish genome.

This sort of nonsense should never be let through peer review anywhere. It makes the ASHG and indeed population genetics look like a total joke. In fact, imagine if such sloppy inferences from population genetics are allowed to influence medical genetics work. Someone might eventually get hurt.
See also...
Finngolians #1R1a and R1b from an early Mongolian tomb

Monday, October 16, 2017

Very soon, perhaps even this year, we'll be seeing a major new paper from Harvard on the population history of South Asia. Apparently it'll be mostly based on ancient DNA from Bronze and Iron Age sites in present-day India and Pakistan. And yes, I know for a fact that it'll include Harappan samples from India.
It has to be said, unfortunately, that nearly all academic efforts to date to crack the mystery of the peopling of South Asia using DNA have been way below par, and often quite farcical. That's because ancient DNA relevant to South Asian population history hasn't been available for very long, and learning about ancient migrations and admixture events exclusively from modern-day DNA is really hard.
Also, I feel that many of these efforts have been ruined by politics. I don't want to harp on about that too much here, but it seems to me that the rather far fetched Out-of-India theory (OIT) has gained traction among many population geneticists of late simply because it's politically more palatable in the west than its main rival, the Aryan Invasion Theory (AIT). And that's mostly because the Nazis had a thing for Aryans, but also because AIT is seen by many Indians as an outdated concept used by the British during colonial times to legitimize their conquest of India.
Indeed, it's been a frustrating experience for me, and many others I'm sure, watching this nonsense unfold for the past 10-15 years. But on a positive note, it's forced me to look at this issue in more detail and produce a lot of solid work. It might be a good time now to recap this work. Below, sorted more or less in terms of awesomeness, is the best of Davidski on South Asia:

These blog posts have already been read by many thousands of people, and, somewhat surprisingly for me, even made a decent splash on social media such as Facebook, Twitter and Reddit. The screen cap below is from a thread at a Desi Reddit community called ABCDesis (see here).

Most of these Desis are highly skeptical of my arguments, which isn't unusual, nor is it surprising, considering the massive amount of anti-AIT/pro-OIT nonsense that has been dumped online in recent years. But I promise, most of my stuff on South Asia will still be relevant after the new Harvard paper touches down.

Thursday, October 12, 2017

By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1, 2, 3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans [4, 5] while others did not contribute to present-day Eurasian populations [3, 6]. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, [1, 7] to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.

Thursday, October 5, 2017

Over at Science at this LINK. Not surprisingly, these four Sunghir individuals are very similar to another Upper Paleolithic Eastern European, Kostenki14, in terms of both genome-wide genetic structure and uniparental markers (Y-haplogroup C1a2, mtDNA-haplogroups U2 and U8c). If you can't access the paper, the supplementary materials are freely available here, and there's a press release here.

Abstract: Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. We demonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

In the late 80s and early 90s, Colin Renfrew presented his Anatolian hypothesis. According to him, the agrarian revolution begun in Anatolia, and from there, it spread out in Europe. He supposed that these farmers were carriers of the Proto-Indo European language, but his theory had weak support from Indo-European linguists. Some questions then arise: What language(s) was introduced in the Ægean islands and mainland Greece by these early farmers? Can we figure out the affiliations of the Minoan language? A different agrarian hypothesis will be shown in these pages, unrelated to the Indo-European and Semitic language families. It instead is featuring a new language family that encompasses the Ægean, Anatolia, Caucasus and the Near East.
...
Both archaeology and genetics point to an agrarian migration to Greece, originating from central/western Anatolia and the fertile crescent. Several millennia later, we find Hattic spoken in central Anatolia, while Hurrian was spoken within a large part of the fertile crescent [13]. Caucasus is nearby and is therefore a possible refuge of people akin to these early farming societies. Linguistic data seem to incline towards the conclusions made by geneticists and archaeologists. The aforementioned migrational model can explain why Pre-Greek words have counterparts in Hattic, Hurro-Urartian and North Caucasian languages. After the Indo-European and Afro-Asiatic linguistic families’ reconstructions, a third big family might emerge from this research. The goal is to restore common roots between those languages. Thus, any finding must be within a framework of rules, the conventional Neogrammarian method that is universally accepted. Rules appear to be static and precise, any Pre-Greek word could have a counterpart with Hattic and/or Hurro-Urartian and/or North Caucasian languages; in all respect, ἀ-> *Ø- is seen in all occasions. There are more rules and lexical data, but they are not mentioned in this paper. This is a proposal for further investigation in Languages and Linguistics, from Bronze Age to present in the region between Asia and Europe.

Tuesday, September 26, 2017

A lot has been written about Y-haplogroup R1a over the years. Sadly, most of it was wrong, such as its posited Pleistocene origin in the Indian subcontinent and subsequent migration to Europe.
In all likelihood, R1a was born somewhere in North Eurasia. More importantly, its R1a-M417 subclade, which encompasses almost 100% of modern-day R1a lineages, no doubt came into existence somewhere on the Pontic-Caspian (or Western) steppe in what is now Ukraine and southern Russia just 7,000-6,000 years ago.
And within a couple of thousand years it expanded in almost all directions, probably on the back of the early Indo-European dispersals (see here), to cover a massive range from Scandinavia to South Asia. It is the beast among Y-haplogroups.

Thursday, September 21, 2017

Over at bioRxiv at this LINK. The paper includes three ancient North African Y-haplogroup results: two instances of E-M35 from the Early Neolithic (5300-4800 BCE) and a singleton T-M184 from the Late Neolithic (3780-3650 BCE). Emphasis is mine:

Abstract: One of the greatest transitions in the human story was the change from hunter-gatherer to farmer. How farming traditions expanded from their birthplace in the Fertile Crescent has always been a matter of contention. Two models were proposed, one involving the movement of people and the other based on the transmission of ideas. Over the last decade, paleogenomics has been instrumental in settling long-disputed archaeological questions, including those surrounding the Neolithic revolution. Compared to the extensive genetic work done on Europe and the Near East, the Neolithic transition in North Africa, including the Maghreb, remains largely uncharacterized. Archaeological evidence suggests this process may have happened through an in situ development from Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. In fact, Neolithic pottery in North Africa strongly resembles that of European cultures like Cardial and Andalusian Early Neolithic, the southern-most early farmer culture from Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic individuals. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region. Among ancient populations, early Neolithic Moroccans share affinities with Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in comparison, share an Iberian component of a prominent European-wide demic expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.

Tuesday, September 19, 2017

A new version of Mathieson et al. 2017 has just been posted at BioRxiv (see here). It includes more samples. One of these new samples is a male from an Eneolithic Sredny Stog culture site on the North Pontic (Ukrainian) steppe who belongs to Y-haplogroup R1a-M417 (ID I6561 from Alexandria in the ADMIXTURE bar graph below). This is huge, obviously with major implications for the peopling of large parts of Eurasia. Why? Because of this. Here's the new abstract:

Abstract: Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2000 years before the migration that replaced much of northern Europe's population.

Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted September 19, 2017, doi: https://doi.org/10.1101/135616
By the way, I don't want to toot my own horn too much, but looking back, some of my comments in the discussion about the first version of Mathieson et al. 2017 were awesome. See here and here.

Three new Yamnaya, all from Ukraine, but sadly all females.
Expected the Mesolithic/Neolithic R1a/R1b in Ukraine, and it would've been good to see some Yamnaya males from there, because some are likely to be R1a-M417.
But it's nice to see that Bulgarian MLBA R1a/U5a sample. Interesting date for R1a to be in the Balkans: 1750-1625 calBCE (3400±30 BP).
...
It can't be a coincide that all of their Yamnaya samples from Ukraine are females.
I reckon they're holding the males back for their South Asian paper.
I'm surprised they let the Bulgarian MLBA R1a out of the bag, because that's a big clue about what we'll see in BA Ukraine.

Update 20/09/2017: I put together a spreadsheet with the key details for the samples in this paper (click on the image below to open it). I'm not sure which of the individuals are new, because many of the IDs have been changed. A spreadsheet with the original set of samples is located here.

Monday, September 18, 2017

I've had a few requests from personal genomics customers to stick their files into an Identity-by-Descent/cM matrix like the one at the link below. Also please check out the accompanying comments thread for ideas of what can be done with the output.
A Bronze Age dominion from the Atlantic to the Altai
I can do this for [] per individual. Please e-mail the data and money (via PayPal) to []. The deadline for sending through the data files (which, in this run, can only be from 23andMe, Ancestry or FTDNA) is this time Tuesday.
I'll send out the results to each participant over e-mail. However, participants are encouraged to post their results in the comments thread below so that they can be discussed and analyzed further.
Update 20/09/2017: The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.
Update 22/09/2017: I've just sent out the results to the participants in the form of two text files titled "ancients_only" and "full_column". The former is a matrix of overall shared haplotype tracts in centimorgans (cM) that includes the user and 65 ancient genomes, and the latter a list of haplotype tracts, also in cM, shared between the user and well over 3000 public samples.
So what can we do with these files? For one, we can look at them, because simply eyeballing these sorts of stats can be very informative. Sorting the data in some way and calculating population averages might help with that.
The "ancients_only" file can be used for slightly more advanced analyses. For instance, below is a Neighbor joining graph produced with the Past 3 program (freely available here). I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view.

Indeed, Past 3 can do a lot of interesting things with matrix files; anything from linear models to rotating three dimensional plots. If you'd like to repeat the linear models from my above linked to blog post, then choose the relevant two columns in your matrix and go Model > Generalized Linear Model. You should see something like this.

Moreover, a matrix with the 3000+ public samples can be gotten here and combined, in part or in whole, with your other files so that you can analyze yourself alongside a larger number of individuals.

Friday, September 15, 2017

What are the historical and linguistic implications of these qpAdm mixture models, apart, of course, from the most obvious? Please share your thoughts in the comments below. By the way, I tried a wide variety of ancients only models for the Greeks and Italians and these were statistically the most sound. If you're wondering who the Roman outlier is, see here.

Wednesday, September 13, 2017

Over at the American Journal of Archaeology at this LINK. Below is the paper abstract. Emphasis is mine.

In this article, we approach the Neolithization of southern Scandinavia from an archaeolinguistic perspective. Farming arrived in Scandinavia with the Funnel Beaker culture by the turn of the fourth millennium B.C.E. It was superseded by the Single Grave culture, which as part of the Corded Ware horizon is a likely vector for the introduction of Indo-European speech. As a result of this introduction, the language spoken by individuals from the Funnel Beaker culture went extinct long before the beginning of the historical record, apparently vanishing without a trace. However, the Indo-European dialect that ultimately developed into Proto-Germanic can be shown to have adopted terminology from a non-Indo-European language, including names for local flora and fauna and important plant domesticates. We argue that the coexistence of the Funnel Beaker culture and the Single Grave culture in the first quarter of the third millennium B.C.E. offers an attractive scenario for the required cultural and linguistic exchange, which we hypothesize took place between incoming speakers of Indo-European and local descendants of Scandinavia’s earliest farmers.

Recent papers in English dealing with the Neolithic transition on the Caspian steppe aren't easy to find, but I managed to dig one up at Documenta Praehistorica: Initial stages of two Neolithisation models in the Lower Volga basin by Alexander Vybornov.
The author describes two highly contrasting Neolithic traditions in this region; one that is essentially a ceramic Mesolithic culture, no doubt practiced by local foragers, and the other a pastroralist culture, probably brought to the steppe by migrants from the south.
I think it's possible that these migrants could have been the main source of the, thus far imprecisely characterized, Caucasus-related ancestry in the potentially Proto-Indo-European Khvalynsk and Yamnaya peoples (see here). But it's hard to argue either way until someone sequences DNA from a few relevant skeletons.

In this paper, two groups of ancient sites located in the Lower Volga River basin are analysed. The first group is linked to the emergence of the oldest pottery in this region, which is one of the most ancient in Europe. The presence of this feature of the ‘Neolithic package’ can be dated to the middle of the 7th millenium BC. A production economy is a particular feature of the second group of sites, which can be dated to the end of the 6th millenium BC. This is one of the earliest pieces of evidence of the existence of domesticated species in Eastern Europe. These two groups of sites show the initial stages of two Neolithisation models in the Lower Volga basin.
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The Neolithisation process in the southern part of the Low Volga region during 6500–5500 BC did not include a producing economy. From the point of view of European researchers, sites of this period could be attributed only to the ‘ceramic Mesolithic’. In the eastern European scientific world, pottery is regarded as a marker of the beginning of the Neolithic era (Oshibkina 1996), which is why these sites were classified as Neolithic.
...
The origin of Prikaspiiskaya culture is reckoned to be connected with the Lower Don region. Some migration from Western Asia could also have occurred. Thus, the Prikaspiiskaya sites in the Lower Volga region represent the second Neolithisation model proposed for this area. The model is connected with the appearance of a producing economy in the milieu of Prikaspiiskaya culture.

Tuesday, September 12, 2017

A review paper at Archaeological and Anthropological Sciences posits that millet and horses arrived in what is now Greece together during the Bronze Age (see here). The author suggests that they may have been introduced via contacts with cultures to the north/northeast of Greece or directly by migrants from the Eurasian steppe. Considering the recent discovery via ancient human DNA that steppe ancestry also spread into the southern Balkans and Mycenae during the Bronze Age (see links below), I'd say the latter scenario is much more likely. I'd also add that millet and horses were probably part of an economic and cultural package expanding along with early Indo-European speakers throughout Eurasia at the time (note, for instance, how important horses are to the early Indo-European pantheon). Here's the review abstract. Emphasis is mine.

Abstract: Archaebotanical evidence for Panicum miliaceum is reviewed for prehistoric Greece including published and unpublished recent finds, providing a basis for exploring the context of the appearance of millet in Greece, the timing of its introduction and cultivation, and its significance in terms of contacts, movement of people, and cultural identity as expressed through culinary practice and food consumption. To this end, the archaeobotanical record is examined together with human isotopic, archaeozoological, and artefactual evidence. Millet is introduced to the northern part of Greece sometime during the end of the 3rd millennium bc and established as a widely used crop during the Late Bronze Age. Isotopic evidence suggests that millet consumption during the Late Bronze Age was not widespread but confined to certain regions, settlements, or individuals. Millet is suggested to reach Greece from the north after its spread westwards from China through Central Asia and the steppes of Eurasia. The timing of the introduction of millet and the horse in northern Greece coincide; the possibility therefore that they are both introduced through contacts with horse breeding cultures cultivating millet in the north and/or northeast is raised. Intensified contact networks during the Bronze Age, linking prehistoric northern Greece to central Europe and the Pontic Steppes, would have opened the way to the introduction of millet, overland via river valleys leading to the Danube, or via maritime routes, linking the Black Sea to the north Aegean. Alternatively, millet could have been introduced by millet-consuming populations, moving southwards from the Eurasian steppes.